Add a `Dirty` boolean to the `ContainerBase` class. This will be set to
true when the container mutates itself (e.g. remove, mergeBack, clear).
The dirty bit is reset when running `PipelineManager.store`.
This commit changes the following method names across the codebase:
* `storeToDisk` -> `store`
* `loadFromDisk` -> `load`
This has been done since the storage is no longer bound to the local
storage.